Structure of PDB 5vsf Chain B Binding Site BS06

Receptor Information
>5vsf Chain B (length=258) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRN
ITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFEC
NHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEY
VGELISDSEADVREEDSYLFDLDGEVYCIDARFYGNVSRFINHHCEPNLV
PVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRC
GSPKCRHS
Ligand information
Ligand ID9HG
InChIInChI=1S/C22H33N5O2/c1-26-11-9-15(10-12-26)23-21-17-13-19(28-3)20(29-4)14-18(17)24-22(25-21)27(2)16-7-5-6-8-16/h13-16H,5-12H2,1-4H3,(H,23,24,25)
InChIKeyYBQHFHPOKHPBRB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c13cc(c(cc1c(NC2CCN(C)CC2)nc(n3)N(C)C4CCCC4)OC)OC
OpenEye OEToolkits 2.0.6CN1CCC(CC1)Nc2c3cc(c(cc3nc(n2)N(C)C4CCCC4)OC)OC
CACTVS 3.385COc1cc2nc(nc(NC3CCN(C)CC3)c2cc1OC)N(C)C4CCCC4
FormulaC22 H33 N5 O2
NameN~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine
ChEMBLCHEMBL4094717
DrugBank
ZINC
PDB chain5vsf Chain B Residue 3006 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5vsf Structure-activity relationship studies of G9a-like protein (GLP) inhibitors.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		D1162 A1165 D1166 D1171 L1174 D1176 R1245 F1246 I1249 K1250
Binding residue
(residue number reindexed from 1)		D157 A160 D161 D166 L169 D171 R237 F238 I241 K242
Annotation score1
Binding affinityMOAD: Kd=94nM
BindingDB: IC50=4.0nM,Kd=94nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y1155 Y1242
Catalytic site (residue number reindexed from 1) Y150 Y234
Enzyme Commision number 2.1.1.-
2.1.1.367: [histone H3]-lysine(9) N-methyltransferase.
Gene Ontology
Molecular Function
GO:0002039 p53 binding
GO:0008270 zinc ion binding
GO:0016279 protein-lysine N-methyltransferase activity
GO:0042054 histone methyltransferase activity
Cellular Component
GO:0005634 nucleus

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:5vsf, PDBe:5vsf, PDBj:5vsf
PDBsum5vsf
PubMed28662962
UniProtQ9H9B1|EHMT1_HUMAN Histone-lysine N-methyltransferase EHMT1 (Gene Name=EHMT1)

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